No, Skull Kid needs to have the Majora's Mask on the entire time. Final Smash would be flinging the moon down on everyone.

Before that happens, allow me to ask a major question...Is the mask a constant part of him? That'll be like demanding Mario has F.L.U.D.D. on all the time, or Peach should carry her parasol for an entire match, or Yoshi should have an infinite amount of eggs trailing him, or Wario should ride his bike around all the time... things like that. Exclusion of a rumored 3DS sequel and the fact that it appeared in Animal Crossing City Folk, Majora's Mask appeared in one game and that was the N64 one. Not anyone's idea of "classic", since it's usually series yet to be represented in Smash Bros. Then there's the comparison to bad guys who appeared more often, like Vaati, and more current and popular ones, like Ghirahim and Demise. Why must a mask, who was THE real villain, not Skull Kid, appear as a constant part of the character, when it could at least be an Assist Trophy?

Not that the mask or Skull Kid could ever make appearances in Smash Bros. as playable characters, however. Ever gauged his importance in the Zelda universe against the importance of other Zelda villains?

And the Final Smash idea is way too impractical. Perhaps a moon would appear, but it'll be suspended way up in space, and it'll occasionally "cry" solid moon tears that target random foes. The moon could also roar at times, pushing other foes offbalance.